sample summary report expansion (#585)

* init commit

* added queries for sample summary table

* change email query for sample summary

* remove value errors for get barcodes

* update sample summaries queries

* change email query for sample summaries

* changes based on feedback, added tests

* resolve ffq conflict

* fix vs_repo

* forgot t for transaction

* fixed wrong import

* fix in/outbound search

microsetta_private_api/admin/admin_impl.py

@@ -29,7 +29,11 @@
     post_daklapack_orders
 from microsetta_private_api import localization
 from microsetta_private_api.admin.sample_summary import per_sample
-from microsetta_private_api.admin.sample_summary import get_barcodes_for
+from microsetta_private_api.admin.sample_summary import \
+    get_barcodes_by_project_id,\
+    get_barcodes_by_kit_ids, get_barcodes_by_emails,\
+    get_barcodes_by_outbound_tracking_numbers,\
+    get_barcodes_by_inbound_tracking_numbers
 from microsetta_private_api.util.melissa import verify_address
 from microsetta_private_api.util.query_builder_to_sql import build_condition
 from werkzeug.exceptions import Unauthorized
@@ -500,12 +504,26 @@ def query_project_barcode_stats(body, token_info, strip_sampleid):
 
 def query_barcode_stats(body, token_info, strip_sampleid):
     validate_admin_access(token_info)
+
+    project_id = None
+
     if 'sample_barcodes' in body:
-        project_id = None
         barcodes = body["sample_barcodes"]
+    elif 'kit_ids' in body:
+        barcodes = get_barcodes_by_kit_ids(body["kit_ids"])
+    elif 'emails' in body:
+        barcodes = get_barcodes_by_emails(body["emails"])
+    elif 'outbound_tracking_numbers' in body:
+        barcodes = get_barcodes_by_outbound_tracking_numbers(
+            body["outbound_tracking_numbers"]
+        )
+    elif 'inbound_tracking_numbers' in body:
+        barcodes = get_barcodes_by_inbound_tracking_numbers(
+            body["inbound_tracking_numbers"]
+        )
     elif 'project_id' in body:
         project_id = body["project_id"]
-        barcodes = get_barcodes_for(project_id)
+        barcodes = get_barcodes_by_project_id(project_id)
 
     unprocessed_barcodes = None
 

microsetta_private_api/admin/sample_summary.py

@@ -7,14 +7,33 @@
 from werkzeug.exceptions import NotFound
 
 
-def get_barcodes_for(project_id):
-    if project_id is None:
-        raise ValueError("project_id must be defined.")
-
+def get_barcodes_by_project_id(project_id):
     with Transaction() as t:
         return AdminRepo(t).get_project_barcodes(project_id)
 
 
+def get_barcodes_by_kit_ids(kit_ids):
+    with Transaction() as t:
+        return AdminRepo(t).get_barcodes_filter(kit_ids=kit_ids)
+
+
+def get_barcodes_by_emails(emails):
+    with Transaction() as t:
+        return AdminRepo(t).get_barcodes_filter(emails=emails)
+
+
+def get_barcodes_by_outbound_tracking_numbers(outbound_tracking_numbers):
+    with Transaction() as t:
+        return AdminRepo(t).get_barcodes_filter(
+            outbound_tracking_numbers=outbound_tracking_numbers)
+
+
+def get_barcodes_by_inbound_tracking_numbers(inbound_tracking_numbers):
+    with Transaction() as t:
+        return AdminRepo(t).get_barcodes_filter(
+            inbound_tracking_numbers=inbound_tracking_numbers)
+
+
 def per_sample(project, barcodes, strip_sampleid):
     summaries = []
     with Transaction() as t:
@@ -38,6 +57,20 @@ def per_sample(project, barcodes, strip_sampleid):
             sample = diag['sample']
             account = diag['account']
             source = diag['source']
+            first_scans_info = diag['scans_info']
+            last_scans_info = diag['latest_scan']
+            if first_scans_info:
+                first_scan_timestamp = first_scans_info[0]['scan_timestamp']
+                first_scan_status = first_scans_info[0]['sample_status']
+            else:
+                first_scan_timestamp = None
+                first_scan_status = None
+            if last_scans_info:
+                latest_scan_timestamp = last_scans_info['scan_timestamp']
+                latest_scan_status = last_scans_info['sample_status']
+            else:
+                latest_scan_timestamp = None
+                latest_scan_status = None
 
             account_email = None if account is None else account.email
             source_type = None if source is None else source.source_type
@@ -94,6 +127,19 @@ def per_sample(project, barcodes, strip_sampleid):
                     sample_date = None
                     sample_time = None
 
+            kit_by_barcode = admin_repo.get_kit_by_barcode([barcode])
+
+            if kit_by_barcode and len(kit_by_barcode) > 0:
+                info = kit_by_barcode[0]
+
+                kit_id_name = info['kit_id']
+                outbound_fedex_tracking = info['outbound_tracking']
+                inbound_fedex_tracking = info['inbound_tracking']
+            else:
+                kit_id_name = None
+                outbound_fedex_tracking = None
+                inbound_fedex_tracking = None
+
             summary = {
                 "sampleid": None if strip_sampleid else barcode,
                 "project": barcode_project,
@@ -106,7 +152,14 @@ def per_sample(project, barcodes, strip_sampleid):
                 "ffq-taken": ffq_taken,
                 "ffq-complete": ffq_complete,
                 "sample-status": sample_status,
-                "sample-received": sample_status is not None
+                "sample-received": sample_status is not None,
+                "first-scan-timestamp": first_scan_timestamp,
+                "first-scan-status": first_scan_status,
+                "latest-scan-timestamp": latest_scan_timestamp,
+                "latest-scan-status": latest_scan_status,
+                "kit-id": kit_id_name,
+                "outbound-tracking": outbound_fedex_tracking,
+                "inbound-tracking": inbound_fedex_tracking,
             }
 
             for status in ["sample-is-valid",

microsetta_private_api/admin/tests/test_admin_repo.py

@@ -1487,3 +1487,137 @@ def test_update_perk_fulfillment_state(self):
                 )
                 obs = cur.fetchone()
                 self.assertFalse(obs[0])
+
+    def test_get_barcodes_filter_kit_ids_success(self):
+        with Transaction() as t:
+            setup_sql = """
+                INSERT INTO barcodes.kit (kit_id, box_id)
+                VALUES ('test1', '0001e15f-4170-4b28-b111-191cd567c347');
+
+                INSERT INTO barcodes.barcode (barcode, kit_id)
+                VALUES ('00001234', 'test1');
+            """
+            with t.cursor() as cur:
+                cur.execute(setup_sql)
+
+            admin_repo = AdminRepo(t)
+
+            barcodes = admin_repo.get_barcodes_filter(kit_ids=['test1'])
+            self.assertEqual(barcodes, ['00001234'])
+
+    def test_get_barcodes_filter_kit_ids_failure(self):
+        with Transaction() as t:
+            admin_repo = AdminRepo(t)
+            barcodes = admin_repo.get_barcodes_filter(kit_ids=['notarealkit'])
+            self.assertEqual(barcodes, [])
+
+    def test_get_barcodes_filter_emails_success(self):
+        with Transaction() as t:
+            setup_sql = """
+                INSERT INTO ag.source (id, account_id,
+                                       source_type, source_name)
+                VALUES ('0003ddfd-4949-4105-90a9-1b1530af5352', %s,
+                        'Human', 'Test Source');
+                INSERT INTO barcodes.kit (kit_id, box_id)
+                VALUES ('test1', '0001e15f-4170-4b28-b111-191cd567c347');
+                INSERT INTO barcodes.barcode (barcode, kit_id)
+                VALUES ('00001234', 'test1');
+                INSERT INTO ag.ag_kit_barcodes (barcode, source_id)
+                VALUES ('00001234', '0003ddfd-4949-4105-90a9-1b1530af5352');
+            """
+            with t.cursor() as cur:
+                cur.execute(setup_sql, (STANDARD_ACCT_ID,))
+
+            admin_repo = AdminRepo(t)
+
+            barcodes = admin_repo.get_barcodes_filter(emails=['[email protected]'])
+            self.assertEqual(barcodes, ['00001234'])
+
+    def test_get_barcodes_filter_emails_failure(self):
+        with Transaction() as t:
+            admin_repo = AdminRepo(t)
+            barcodes = admin_repo.get_barcodes_filter(
+                emails=['[email protected]'])
+            self.assertEqual(barcodes, [])
+
+    def test_get_barcodes_filter_outbound_tracking_success(self):
+        with Transaction() as t:
+            setup_sql = """
+                INSERT INTO barcodes.kit (kit_id, box_id,
+                        outbound_fedex_tracking)
+                VALUES ('test1', '0001e15f-4170-4b28-b111-191cd567c347',
+                        '12345');
+                INSERT INTO barcodes.barcode (barcode, kit_id)
+                VALUES ('00001234', 'test1');
+            """
+            with t.cursor() as cur:
+                cur.execute(setup_sql)
+
+            admin_repo = AdminRepo(t)
+
+            barcodes = \
+                admin_repo.get_barcodes_filter(
+                    outbound_tracking_numbers=['12345'])
+            self.assertEqual(barcodes, ['00001234'])
+
+    def test_get_barcodes_filter_outbound_tracking_failure(self):
+        with Transaction() as t:
+            admin_repo = AdminRepo(t)
+            barcodes = admin_repo.get_barcodes_filter(
+                outbound_tracking_numbers=['99999'])
+            self.assertEqual(barcodes, [])
+
+    def test_get_barcodes_filter_inbound_tracking_success(self):
+        with Transaction() as t:
+            setup_sql = """
+                INSERT INTO barcodes.kit (kit_id, box_id,
+                    inbound_fedex_tracking)
+                VALUES ('test1', '0001e15f-4170-4b28-b111-191cd567c347',
+                        '67890');
+                INSERT INTO barcodes.barcode (barcode, kit_id)
+                VALUES ('00001234', 'test1');
+            """
+            with t.cursor() as cur:
+                cur.execute(setup_sql)
+
+            admin_repo = AdminRepo(t)
+
+            barcodes = admin_repo.get_barcodes_filter(
+                inbound_tracking_numbers=['67890'])
+            self.assertEqual(barcodes, ['00001234'])
+
+    def test_get_barcodes_filter_inbound_tracking_failure(self):
+        with Transaction() as t:
+            admin_repo = AdminRepo(t)
+            barcodes = admin_repo.get_barcodes_filter(
+                inbound_tracking_numbers=['99999'])
+            self.assertEqual(barcodes, [])
+
+    def test_get_kit_by_barcode_success(self):
+        with Transaction() as t:
+            setup_sql = """
+                INSERT INTO barcodes.kit (kit_id, box_id)
+                VALUES ('test1', '0001e15f-4170-4b28-b111-191cd567c348');
+
+                INSERT INTO barcodes.barcode (barcode, kit_id)
+                VALUES ('00001234', 'test1');
+            """
+            with t.cursor() as cur:
+                cur.execute(setup_sql)
+
+            admin_repo = AdminRepo(t)
+
+            kit_info = admin_repo.get_kit_by_barcode(['00001234'])
+            expected = [{
+                'barcode': '00001234',
+                'outbound_tracking': None,
+                'inbound_tracking': None,
+                'kit_id': 'test1'
+            }]
+            self.assertEqual(kit_info, expected)
+
+    def test_get_kit_by_barcode_failure(self):
+        with Transaction() as t:
+            admin_repo = AdminRepo(t)
+            kit_info = admin_repo.get_kit_by_barcode(['nonexistent_barcode'])
+            self.assertIsNone(kit_info)

microsetta_private_api/api/microsetta_private_api.yaml

@@ -2998,6 +2998,22 @@ paths:
                     # not using the defined schema for sample_barcode as it is
                     # readOnly
                     type: string
+                'kit_ids':
+                  type: array
+                  items:
+                    type: string
+                'emails':
+                  type: array
+                  items:
+                    type: string
+                'outbound_tracking_numbers':
+                  type: array
+                  items:
+                    type: string
+                'inbound_tracking_numbers':
+                  type: array
+                  items:
+                    type: string
       responses:
         '200':
           description: Return an object containing a list of dictionaries of sample status for requested accounts